Okay, I will create a Obito STORY for you guys and see if this fits for a motive.
In regards to Obito being crushed by the rock.
At this point we know Obito unlocks his sharingan. Tobi is able to phase in and out of objects (by moving parts of himself to another dimension) only possessing the sharingan, its not an MS technique. You never see his eye change to MS when he does this.
Enters Obito, Rin, kakashi and the boulder: Obito can not feel the right side of his body as he lies under rock, at this point he is unaware of his sharingans abilities and he subconciously sent that part of his body to the other dimension to protect himself. He cant feel the right side of his body because it isnt there anymore and this happens to be part of the ability to sustain his life while dodging "attacks". The last thing he asks of Kakashi is to protect Rin from now on. Rin and Kakashi leave and Obito lies there for a day before he realizes he's not dying yet. It doesnt make sense. He tries to stand up and realizes his body phases right through the boulder!!!!.
At this point he decides not to go back to Konoha as he knows the person he loves, loves Kakashi and he doesnt want to get in the way, I mean why not, right? They think he's dead and it might be better off that way for Rin to move on so he feels in his heart, but he continues to watch from afar. he continues to master his ninjitsu ability, mainly his sharingan.
In regards to the comment about Kakashi standing in front of the grave from Tobi.
Fast forward to the Ninja war, the battle place is the bridge. Kakashi and Rin are stopping the invading Ninja army at the bridge, Obito does not participate in this war but is still watching after his true love, Rin. A tactic by the invading Ninja army is used to decieve Kakashi and launch an incoming fatal assault to Rin. Obito sees this attack all too clearly and is confindent that Kakashi also sees it coming and decides not to interfere. He was wrong. He sees Rin ran through and killed right before him. Kakashi is in a state of shock followed by a state of Rage!!!
Kakashi goes on a vengeful assault, basically holding off the invading ninja army by himself.
In the meantime, Obito goes through a mental breakdown. He starts wondering what if would the outcome have been if he interfered and revealed that he was alive to Rin. That she would have been happy to see him and glad he saved her. He starts to grow alot of resentment and anger to Kakashi, to the leaf for that fact for not reinforcing this obvious weakness in the bridge. He feels in his heart by letting Rin die, he in fact killed her himself...
In regards to the comment made by Kakashi and Tobi with reference to the Battle at the Bridge 
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He unlocks his MS ability. He unknowingling transports himself to the other dimension and reappears back on the other side of the bridge behind enemy lines while kakashi hold them off. In his own fit of rage, Obito slays each and every ninja that he comes across. It is literally a one sided fight and every attack passes through him without harming him, he ends up transporting a small group of the ninjas to the alternate reality where he fights them on his own turf. The leader of the invading army and kakashi both witness this. Fear is struck into the invading ninja army as they havent a clue where their commrades went. This technique was the first of its kind witnessed in such a massive exodus of ninja into the void.
From Kakashi's perspective he saw an unknown fighter battling multiple ninja and witnessed adept skills in dodging on going attacks as if they passed right through him, from his perspective and the location he was, he could only see shadow fighting. When he was done his the small force at the bridge he moved forward to see who his "ally" was but he only found some bodies. Obito had already phased back out of the fight and back to the shadows. Kakashi at this point has no idea who it was and decides to keep it a secret. Kakashi becomes the Hero of the leaf. At this point Obito decides he is going to get back at the Leaf, for letting "her die". This includes all members of the leaf including uchiha, whom he never really had a care for since they didnt look at him as an Uchiha.
In regards to, "How did Nagato get the Rinnegan?!?!? Obito was too young to be the giver of the eyes."
During this time period Obito meets another with the same ideals. This other character happens to be in possession of a Sharingan as well, he was older Uchiha whom captured the Hidden mists kage and provided Madara's Rinnegan to Nagato during the war back in the day. This man wore a mask (white mask much like Leaf special unit but with one eye hole) and told him of a small group he needs him to become involved with. The masked man already has some involvement with this group, the Akatski. As he was the one who originally forced its developement from the shadows. In order for Obito to enter into the Atkatski and pull it off as replacing the masked mans involvement (at this point names were not shared between the masked man and Nagato's group). Why does the mask man need his help? well because he's getting really old, he is in fact Madara Uchiha whom everyone thought had died during the battle with hashirama. Obito is suppose to carry on the character of the masked man while carrying out Madara's plan (to revive Madara in the near future). At this point Obito knows about the Rinnegan and its abilities.
Tobi is born and the Akatski is manipulated from within. Ideals become twisted to follow Tobi's plan. Knowing how important information is, Tobi changes his character and role in the Akatski so some enemies never catch on to who he is and what he is, a.k.a Orochimaru who's looking to get a hold of a Sharingan. Last thing Tobi wants is to become a target from another treacherous Akatski member. As Tobi's ability is unheard of in the Ninja world, Tobi enters the Leaf village and overhears a rumor in the Uchiha that their maybe a Coup de Tat to take over the Leaf. This is golden information. He goes ahead and "accidentally reveals" the plan to leaf ninja either within the village or out in the field and then he watches... You know the rest.
This is what I feel might be a good reason why Obito CAN be Tobi. There it is, an Obito Theory that isnt short, and shares enough reasons and ideas to possibly make it stick
So if Madara gave his eyes to Nagato, what did he control the mist kage with???
Madara was a collector of the sharingans at the time, he had already had his eyes transplanted in order to give the Rinnegan to Nagato. The collection continues when Obito Tobi collects the assortment from other various uchiha including the Uchiha massacre. Im sure some of the Uchiha had their sharingan out in full flare, not all were killed in their sleep.
What about Zetsu? I havent a clue. lol. He's more unknown than Tobi is at this point. He seems to be a henchman for "the Tobi's / masked men". Its possible that he was even around since Madara.
We will save ideas about Zetsu for the Zetsu Theories Threads. This is an Obito Theory Thread.
Of course madara did die, could be from natural causes, or his old battle wounds. He was weakened after his fight Im sure.
